Loading Library

library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)

Simulating MPEA Surrogate over the array.

load(file = "diabetes_curated.Rdata")
epsilon=1e-6
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (epsilon+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
## KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP 
##                          0.0000000001 
##            GROSS_HYPOXIA_VIA_HIF1A_UP 
##                          0.0002000001 
##               WHITFIELD_CELL_CYCLE_G2 
##                          0.0002000001 
##         MA_MYELOID_DIFFERENTIATION_DN 
##                          0.0003000001 
##   CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP 
##                          0.0004000001 
##       REACTOME_CHROMOSOME_MAINTENANCE 
##                          0.0005000001 
##            WIERENGA_STAT5A_TARGETS_UP 
##                          0.0006000001 
##             REACTOME_MEIOTIC_SYNAPSIS 
##                          0.0009000001 
##                      REACTOME_MEIOSIS 
##                          0.0010000001 
##      MORI_SMALL_PRE_BII_LYMPHOCYTE_UP 
##                          0.0010000001
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
length(dcor_significant_pathways_p.value)
## [1] 251
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
length((nominal_dcor_q_values_under_25))
## [1] 3
nominal_dcor_q_values_under_25
## KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP 
##                          0.0000003525 
##            GROSS_HYPOXIA_VIA_HIF1A_UP 
##                          0.2350001175 
##               WHITFIELD_CELL_CYCLE_G2 
##                          0.2350001175

GSEA signifcanct pathways p-value and Q-value

nrow(gsea_results_significant)
## [1] 170
length(rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
## [1] 0

Identifying the pathways deemed significant in both GSEA and MPEA

Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))

Mutually_identified_in_GSEA_dcor
##  [1] "GROSS_HYPOXIA_VIA_HIF1A_UP"                           
##  [2] "REACTOME_CHROMOSOME_MAINTENANCE"                      
##  [3] "REACTOME_MEIOTIC_SYNAPSIS"                            
##  [4] "REACTOME_MEIOSIS"                                     
##  [5] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP"
##  [6] "MORI_IMMATURE_B_LYMPHOCYTE_UP"                        
##  [7] "LANDIS_ERBB2_BREAST_TUMORS_65_UP"                     
##  [8] "SMID_BREAST_CANCER_ERBB2_UP"                          
##  [9] "REACTOME_MRNA_CAPPING"                                
## [10] "FERRANDO_TAL1_NEIGHBORS"                              
## [11] "REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER"            
## [12] "REACTOME_NUCLEOTIDE_EXCISION_REPAIR"                  
## [13] "OHGUCHI_LIVER_HNF4A_TARGETS_UP"                       
## [14] "GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP"                
## [15] "PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP"                 
## [16] "WONG_MITOCHONDRIA_GENE_MODULE"                        
## [17] "SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER"    
## [18] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN"                
## [19] "KEGG_OXIDATIVE_PHOSPHORYLATION"                       
## [20] "KEGG_HUNTINGTONS_DISEASE"                             
## [21] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13"     
## [22] "REACTOME_DNA_REPAIR"                                  
## [23] "MOOTHA_VOXPHOS"
Mutually_identified_in_GSEA_dcor_fdr <- intersect(names(nominal_dcor_q_values_under_25),rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
length(Mutually_identified_in_GSEA_dcor_fdr)
## [1] 0

Identifying the pathways significant in MPEA not in GSEA

Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP WHITFIELD_CELL_CYCLE_G2 MA_MYELOID_DIFFERENTIATION_DN CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP WIERENGA_STAT5A_TARGETS_UP MORI_SMALL_PRE_BII_LYMPHOCYTE_UP SHEPARD_CRUSH_AND_BURN_MUTANT_UP HEIDENBLAD_AMPLICON_12P11_12_UP WANG_TARGETS_OF_MLL_CBP_FUSION_DN FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP ZHANG_TLX_TARGETS_60HR_DN BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN SMITH_TERT_TARGETS_DN GEORGES_TARGETS_OF_MIR192_AND_MIR215 ZHENG_FOXP3_TARGETS_IN_THYMUS_UP FRIDMAN_IMMORTALIZATION_DN LEE_DIFFERENTIATING_T_LYMPHOCYTE MITSIADES_RESPONSE_TO_APLIDIN_UP FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS FOSTER_TOLERANT_MACROPHAGE_UP ENK_UV_RESPONSE_KERATINOCYTE_DN IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER WALLACE_PROSTATE_CANCER_RACE_UP PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 WIERENGA_STAT5A_TARGETS_GROUP1 ENGELMANN_CANCER_PROGENITORS_DN HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN OUILLETTE_CLL_13Q14_DELETION_DN FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP CAFFAREL_RESPONSE_TO_THC_DN PID_EPHA_FWDPATHWAY BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP BHAT_ESR1_TARGETS_VIA_AKT1_UP OISHI_CHOLANGIOMA_STEM_CELL_LIKE_DN LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP PID_PTP1B_PATHWAY BIOCARTA_PAR1_PATHWAY GARY_CD5_TARGETS_DN BIOCARTA_CARDIACEGF_PATHWAY QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2 JAEGER_METASTASIS_DN REACTOME_PI3K_AKT_ACTIVATION BROWNE_HCMV_INFECTION_48HR_UP WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA BORCZUK_MALIGNANT_MESOTHELIOMA_UP REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING LIU_PROSTATE_CANCER_UP FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL GEISS_RESPONSE_TO_DSRNA_DN HORTON_SREBF_TARGETS KEGG_RNA_POLYMERASE REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5 PID_PRL_SIGNALING_EVENTS_PATHWAY FORTSCHEGGER_PHF8_TARGETS_UP HOUSTIS_ROS ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN KEGG_STEROID_BIOSYNTHESIS SANSOM_APC_TARGETS_DN LABBE_WNT3A_TARGETS_DN BOCHKIS_FOXA2_TARGETS REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING CHEBOTAEV_GR_TARGETS_DN VERHAAK_GLIOBLASTOMA_NEURAL MACLACHLAN_BRCA1_TARGETS_UP PID_EPHA2_FWD_PATHWAY DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE BIOCARTA_CDC42RAC_PATHWAY NAGASHIMA_NRG1_SIGNALING_DN TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP PLASARI_TGFB1_TARGETS_10HR_DN REACTOME_REGULATORY_RNA_PATHWAYS PID_S1P_S1P3_PATHWAY DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP PID_TGFBR_PATHWAY PLASARI_NFIC_TARGETS_BASAL_UP SHI_SPARC_TARGETS_UP PID_S1P_S1P1_PATHWAY KEGG_PYRIMIDINE_METABOLISM MULLIGHAN_NPM1_SIGNATURE_3_UP PID_LIS1_PATHWAY PID_S1P_S1P2_PATHWAY REACTOME_MICRORNA_MIRNA_BIOGENESIS HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS BROWNE_HCMV_INFECTION_6HR_DN PID_AVB3_INTEGRIN_PATHWAY PID_ECADHERIN_KERATINOCYTE_PATHWAY PETRETTO_CARDIAC_HYPERTROPHY CHEN_ETV5_TARGETS_TESTIS SHEN_SMARCA2_TARGETS_UP REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING BROWNE_HCMV_INFECTION_4HR_DN PID_WNT_NONCANONICAL_PATHWAY DAZARD_RESPONSE_TO_UV_NHEK_DN RIGGI_EWING_SARCOMA_PROGENITOR_DN PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP BIOCARTA_RAS_PATHWAY MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN SA_TRKA_RECEPTOR REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE PID_SYNDECAN_4_PATHWAY PETROVA_PROX1_TARGETS_UP GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN GAJATE_RESPONSE_TO_TRABECTEDIN_UP REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP BERNARD_PPAPDC1B_TARGETS_UP NUYTTEN_NIPP1_TARGETS_UP KASLER_HDAC7_TARGETS_1_DN MENSE_HYPOXIA_UP KENNY_CTNNB1_TARGETS_DN ONDER_CDH1_TARGETS_1_UP BASAKI_YBX1_TARGETS_UP WINZEN_DEGRADED_VIA_KHSRP RODWELL_AGING_KIDNEY_NO_BLOOD_DN MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP PID_P53_REGULATION_PATHWAY WIERENGA_STAT5A_TARGETS_GROUP2 UEDA_PERIFERAL_CLOCK WANG_SMARCE1_TARGETS_UP PID_ECADHERIN_NASCENT_AJ_PATHWAY BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY WINNEPENNINCKX_MELANOMA_METASTASIS_DN REACTOME_G_ALPHA1213_SIGNALLING_EVENTS LEIN_CHOROID_PLEXUS_MARKERS TARTE_PLASMA_CELL_VS_PLASMABLAST_DN LIN_NPAS4_TARGETS_UP NADLER_HYPERGLYCEMIA_AT_OBESITY SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP JOHNSTONE_PARVB_TARGETS_3_UP RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP COATES_MACROPHAGE_M1_VS_M2_DN MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP PENG_RAPAMYCIN_RESPONSE_UP BILD_MYC_ONCOGENIC_SIGNATURE MCCLUNG_COCAINE_REWARD_5D HU_ANGIOGENESIS_DN LENAOUR_DENDRITIC_CELL_MATURATION_DN ODONNELL_METASTASIS_DN CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP PETRETTO_HEART_MASS_QTL_CIS_DN MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP CADWELL_ATG16L1_TARGETS_DN VANTVEER_BREAST_CANCER_ESR1_UP MASSARWEH_RESPONSE_TO_ESTRADIOL DE_YY1_TARGETS_UP GUILLAUMOND_KLF10_TARGETS_DN BIOCARTA_EDG1_PATHWAY ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER MARKS_HDAC_TARGETS_UP NOJIMA_SFRP2_TARGETS_UP BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN HASLINGER_B_CLL_WITH_MUTATED_VH_GENES BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS LIU_SOX4_TARGETS_UP BIOCARTA_RACCYCD_PATHWAY FARMER_BREAST_CANCER_APOCRINE_VS_BASAL SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP PUJANA_BRCA2_PCC_NETWORK SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5 REACTOME_MRNA_SPLICING_MINOR_PATHWAY REACTOME_RNA_POL_III_TRANSCRIPTION COATES_MACROPHAGE_M1_VS_M2_UP AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER AMIT_EGF_RESPONSE_40_MCF10A GOLUB_ALL_VS_AML_DN MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN CUI_GLUCOSE_DEPRIVATION MOREIRA_RESPONSE_TO_TSA_UP GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP RICKMAN_METASTASIS_UP BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN MANALO_HYPOXIA_DN BIOCARTA_P53HYPOXIA_PATHWAY YAMASHITA_METHYLATED_IN_PROSTATE_CANCER GUTIERREZ_MULTIPLE_MYELOMA_UP BIOCARTA_PTDINS_PATHWAY VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 TIAN_TNF_SIGNALING_NOT_VIA_NFKB VARELA_ZMPSTE24_TARGETS_UP LI_INDUCED_T_TO_NATURAL_KILLER_DN MURAKAMI_UV_RESPONSE_6HR_DN PID_AVB3_OPN_PATHWAY REACTOME_PEROXISOMAL_LIPID_METABOLISM SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED BRUECKNER_TARGETS_OF_MIRLET7A3_UP ENGELMANN_CANCER_PROGENITORS_UP YAGI_AML_WITH_T_8_21_TRANSLOCATION YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1 GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP PID_VEGFR1_2_PATHWAY LAMB_CCND1_TARGETS LEE_TARGETS_OF_PTCH1_AND_SUFU_DN MURAKAMI_UV_RESPONSE_24HR GENTILE_UV_LOW_DOSE_UP KEGG_COLORECTAL_CANCER KEEN_RESPONSE_TO_ROSIGLITAZONE_UP ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP PID_IL4_2PATHWAY JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP MISSIAGLIA_REGULATED_BY_METHYLATION_UP REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT YAGI_AML_RELAPSE_PROGNOSIS BURTON_ADIPOGENESIS_6 REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT MIKKELSEN_ES_ICP_WITH_H3K4ME3 REACTOME_CHOLESTEROL_BIOSYNTHESIS
MPEA 0.0000 0.0002 0.0003 0.0004 0.0006 0.0010 0.0010 0.0011 0.0011 0.0014 0.0014 0.0017 0.0019 0.0020 0.0021 0.0025 0.0028 0.0030 0.0032 0.0033 0.0034 0.0035 0.0036 0.0039 0.004 0.0046 0.0049 0.0051 0.0058 0.0059 0.0061 0.0061 0.0062 0.0064 0.0066 0.0073 0.0079 0.0080 0.0081 0.0085 0.0090 0.0093 0.0094 0.0098 0.010 0.0101 0.0102 0.0104 0.0108 0.0110 0.0116 0.0118 0.0118 0.0118 0.0118 0.0120 0.0124 0.0124 0.0127 0.0127 0.0134 0.0138 0.0141 0.0147 0.0147 0.0149 0.0150 0.0153 0.0153 0.0158 0.0162 0.0162 0.0164 0.0169 0.0171 0.0171 0.0173 0.0174 0.0176 0.0178 0.0178 0.0179 0.0180 0.0183 0.0184 0.0186 0.0187 0.0189 0.0192 0.0193 0.0197 0.0198 0.020 0.0201 0.0201 0.0203 0.0206 0.0208 0.0208 0.0210 0.0211 0.0211 0.0213 0.0219 0.0220 0.0223 0.0224 0.0224 0.0225 0.0228 0.0231 0.0236 0.0241 0.0245 0.0247 0.0251 0.0251 0.0251 0.0253 0.0253 0.0255 0.0259 0.0261 0.0262 0.0262 0.0264 0.0266 0.0267 0.0270 0.0271 0.0275 0.0277 0.0280 0.0283 0.0283 0.0284 0.0285 0.0288 0.0289 0.0290 0.0291 0.0294 0.0299 0.0300 0.0303 0.0303 0.0305 0.0306 0.0323 0.0323 0.0331 0.0334 0.0335 0.0339 0.0339 0.0339 0.0340 0.0346 0.0346 0.0347 0.0347 0.0348 0.0353 0.0354 0.0355 0.0355 0.0356 0.036 0.0361 0.0362 0.0363 0.0367 0.0370 0.0371 0.0372 0.0372 0.0375 0.0377 0.0379 0.0379 0.0382 0.0384 0.0386 0.0389 0.0389 0.0395 0.0399 0.0399 0.0400 0.0401 0.0410 0.0410 0.0412 0.0415 0.0416 0.0418 0.0422 0.0422 0.0429 0.0432 0.0433 0.0436 0.0436 0.0441 0.0442 0.0445 0.0445 0.0447 0.0448 0.0452 0.0452 0.0453 0.0454 0.0457 0.0460 0.0469 0.0471 0.0472 0.0474 0.048 0.0481 0.0483 0.0485 0.0485 0.0488 0.0491 0.0491 0.0499
GSEA 0.7939 0.9876 0.2189 0.2354 0.2618 0.5202 0.1169 0.5246 0.7294 0.1394 0.1515 0.6320 0.3854 0.2096 0.8133 0.7462 0.7427 0.0977 0.6335 0.3752 0.6447 0.9084 0.4907 0.7976 0.497 0.2470 0.7563 0.5545 0.1467 0.7864 0.2458 0.7019 0.3020 0.8959 0.2016 0.7410 0.5279 0.2785 0.9792 0.2609 0.3593 0.4626 0.6437 0.8517 0.917 0.4706 0.1566 0.0541 0.2172 0.8423 0.1959 0.1481 0.7030 0.0813 0.6083 0.3138 0.1454 0.3533 0.2560 0.6378 0.2281 0.6826 0.1972 0.8822 0.4839 0.2924 0.0671 0.2548 0.3777 0.5885 0.2110 0.7505 0.3730 0.6747 0.7375 0.1127 0.1750 0.9283 0.4038 0.9014 0.8059 0.7820 0.4008 0.9248 0.3119 0.3037 0.3267 0.3840 0.2688 0.4038 0.9648 0.0855 0.996 0.3123 0.8800 0.5264 0.8546 0.9123 0.6963 0.4346 0.5838 1.0000 0.7234 0.9403 0.2385 0.0638 0.4255 0.2464 0.4812 0.8540 0.6598 0.5322 0.7256 0.1713 0.3733 0.0601 0.4369 0.6982 0.0890 0.7206 0.2758 0.4942 0.7146 0.4047 0.6371 0.0569 0.5078 0.3551 0.6593 0.9724 0.5445 0.3631 0.4124 0.1904 0.7666 0.0881 0.9053 0.6093 0.5515 0.7196 0.2358 0.8516 0.8760 0.6968 0.3984 0.7784 0.8869 0.8103 0.0678 0.7992 0.4688 0.9772 0.1475 0.8377 0.6754 0.7947 0.2093 0.1357 0.3680 0.8806 0.3840 0.3041 0.5219 0.7025 0.2772 0.7202 0.0972 0.666 0.4286 0.6250 0.9593 0.4838 0.4038 0.8337 0.5215 0.7515 0.1794 0.7442 0.4199 0.5193 0.7146 0.0754 0.2063 0.6245 0.2231 0.6068 0.4928 0.4052 0.6223 0.5386 0.0547 0.5592 0.8244 0.8613 0.4118 0.2604 0.9941 0.2965 0.7084 0.1155 0.2920 0.1187 0.4714 0.6888 0.6701 0.7667 0.8939 0.5984 0.8178 0.2564 0.8735 0.2615 0.3401 0.5937 0.8621 0.7918 0.3490 0.8487 0.1116 0.657 0.6230 0.8665 0.2460 0.7898 0.1412 0.0587 0.6858 0.5293

Identifying the pathways significant in GSEA not in MPEA

Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
LUI_TARGETS_OF_PAX8_PPARG_FUSION LUI_THYROID_CANCER_CLUSTER_3 ANDERSEN_LIVER_CANCER_KRT19_UP REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_ POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN MCBRYAN_PUBERTAL_BREAST_3_4WK_DN REACTOME_INFLUENZA_LIFE_CYCLE LANDIS_ERBB2_BREAST_TUMORS_324_UP KEGG_ALZHEIMERS_DISEASE REACTOME_METABOLISM_OF_RNA CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP REACTOME_RESPIRATORY_ELECTRON_TRANSPORT FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY REACTOME_METABOLISM_OF_MRNA PECE_MAMMARY_STEM_CELL_UP KEGG_NUCLEOTIDE_EXCISION_REPAIR TONG_INTERACT_WITH_PTTG1 EHLERS_ANEUPLOIDY_UP YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP KANNAN_TP53_TARGETS_DN DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX REACTOME_TRANSLATION REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES TAKAO_RESPONSE_TO_UVB_RADIATION_UP BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE HUMMERICH_BENIGN_SKIN_TUMOR_UP HSIAO_HOUSEKEEPING_GENES JAZAG_TGFB1_SIGNALING_UP BAE_BRCA1_TARGETS_UP KEGG_RIBOSOME NUTT_GBM_VS_AO_GLIOMA_DN MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN REACTOME_METABOLISM_OF_PROTEINS BILANGES_SERUM_RESPONSE_TRANSLATION LANDIS_BREAST_CANCER_PROGRESSION_UP NAKAYAMA_FGF2_TARGETS HUNSBERGER_EXERCISE_REGULATED_GENES LUI_THYROID_CANCER_PAX8_PPARG_DN WENG_POR_TARGETS_GLOBAL_UP REACTOME_PEPTIDE_CHAIN_ELONGATION NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON IRITANI_MAD1_TARGETS_DN YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17 LEE_LIVER_CANCER_SURVIVAL_DN REACTOME_SIGNAL_AMPLIFICATION WANG_RESPONSE_TO_FORSKOLIN_UP JIANG_AGING_HYPOTHALAMUS_UP PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP KEGG_BASAL_TRANSCRIPTION_FACTORS OSMAN_BLADDER_CANCER_DN YANG_BREAST_CANCER_ESR1_UP ZHAN_MULTIPLE_MYELOMA_HP_UP PARK_HSC_MARKERS REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS WANG_TUMOR_INVASIVENESS_UP REACTOME_GLOBAL_GENOMIC_NER_GG_NER GEORGES_CELL_CYCLE_MIR192_TARGETS MAINA_VHL_TARGETS_DN CHEN_PDGF_TARGETS SCHRAMM_INHBA_TARGETS_DN FAELT_B_CLL_WITH_VH3_21_DN BOUDOUKHA_BOUND_BY_IGF2BP2 NATSUME_RESPONSE_TO_INTERFERON_BETA_DN REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN MURAKAMI_UV_RESPONSE_1HR_UP PID_PI3K_PLC_TRK_PATHWAY REACTOME_ADP_SIGNALLING_THROUGH_P2RY1 WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP CHANGOLKAR_H2AFY_TARGETS_UP BIDUS_METASTASIS_DN BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN BORLAK_LIVER_CANCER_EGF_UP REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 KIM_MYC_AMPLIFICATION_TARGETS_UP LINDGREN_BLADDER_CANCER_CLUSTER_1_UP CHANGOLKAR_H2AFY_TARGETS_DN HORIUCHI_WTAP_TARGETS_DN SASAKI_ADULT_T_CELL_LEUKEMIA GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN REACTOME_INTEGRATION_OF_ENERGY_METABOLISM DELASERNA_MYOD_TARGETS_UP KASLER_HDAC7_TARGETS_2_DN PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN SHIN_B_CELL_LYMPHOMA_CLUSTER_8 DOANE_BREAST_CANCER_ESR1_DN BIOCARTA_AGR_PATHWAY REACTOME_RNA_POL_I_PROMOTER_OPENING REACTOME_HDL_MEDIATED_LIPID_TRANSPORT FAELT_B_CLL_WITH_VH3_21_UP KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 HASLINGER_B_CLL_WITH_6Q21_DELETION KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN KEGG_PPAR_SIGNALING_PATHWAY REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE MIKKELSEN_MEF_LCP_WITH_H3K27ME3 XU_GH1_EXOGENOUS_TARGETS_DN ABE_VEGFA_TARGETS_2HR FIGUEROA_AML_METHYLATION_CLUSTER_1_DN REACTOME_LIPOPROTEIN_METABOLISM BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN BIOCARTA_UCALPAIN_PATHWAY ST_T_CELL_SIGNAL_TRANSDUCTION DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY HUMMERICH_MALIGNANT_SKIN_TUMOR_DN CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP PID_NCADHERIN_PATHWAY HUMMERICH_BENIGN_SKIN_TUMOR_DN REACTOME_PACKAGING_OF_TELOMERE_ENDS LEI_HOXC8_TARGETS_DN PID_BARD1_PATHWAY FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP BIOCARTA_MAL_PATHWAY XU_AKT1_TARGETS_6HR PID_INSULIN_GLUCOSE_PATHWAY REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS SA_B_CELL_RECEPTOR_COMPLEXES SCHEIDEREIT_IKK_INTERACTING_PROTEINS REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP RIZ_ERYTHROID_DIFFERENTIATION_HEMGN MEISSNER_BRAIN_HCP_WITH_H3K27ME3 REACTOME_SEMAPHORIN_INTERACTIONS KUMAR_AUTOPHAGY_NETWORK SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN KENNY_CTNNB1_TARGETS_UP OXFORD_RALA_OR_RALB_TARGETS_UP LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP MIKKELSEN_NPC_HCP_WITH_H3K27ME3 BIOCARTA_HER2_PATHWAY FIGUEROA_AML_METHYLATION_CLUSTER_3_DN KYNG_DNA_DAMAGE_BY_4NQO MULLIGHAN_NPM1_SIGNATURE_3_DN PID_IL23_PATHWAY REACTOME_MEIOTIC_RECOMBINATION MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP QI_HYPOXIA
MPEA 0.3242 0.3169 0.6956 0.0577 0.3964 0.2715 0.6418 0.1277 0.0665 0.6026 0.5402 0.0833 0.3190 0.2233 0.6035 0.6305 0.1524 0.6864 0.4786 0.6865 0.6018 0.4589 0.1582 0.6642 0.6234 0.8495 0.1709 0.1870 0.6512 0.2299 0.6299 0.274 0.0948 0.6750 0.4590 0.2537 0.5339 0.5090 0.4730 0.8673 0.0657 0.8722 0.3549 0.6906 0.6585 0.4450 0.1963 0.1226 0.5119 0.4131 0.1975 0.7851 0.1568 0.3937 0.2215 0.4918 0.7278 0.5095 0.6897 0.1328 0.4148 0.0978 0.2645 0.1632 0.0976 0.1489 0.0918 0.4091 0.7153 0.1259 0.0923 0.1369 0.8203 0.4541 0.6576 0.2362 0.0551 0.0797 0.4075 0.2479 0.5201 0.4268 0.1940 0.3909 0.929 0.1703 0.1806 0.6394 0.2736 0.936 0.3609 0.7809 0.676 0.6122 0.9764 0.5319 0.0598 0.629 0.3255 0.9589 0.9908 0.2109 0.9279 0.9903 0.5961 0.5957 0.4794 0.2058 0.7918 0.9702 0.1155 0.5746 0.8472 0.937 0.9869 0.8236 0.9576 0.5793 0.6348 0.9058 0.9774 0.9449 0.2072 0.5027 0.6089 0.9481 0.5256 0.8768 0.5279 0.9091 0.4482 0.1135 0.7895 0.6251 0.0716 0.3927 0.9084 0.2451 0.1464 0.5465 0.0748 0.8108 0.1961 0.4147 0.2857 0.2419 0.5951
GSEA 0.0020 0.0040 0.0040 0.0177 0.0020 0.0019 0.0158 0.0000 0.0121 0.0198 0.0199 0.0141 0.0061 0.0100 0.0355 0.0326 0.0115 0.0219 0.0161 0.0256 0.0124 0.0166 0.0020 0.0321 0.0325 0.0059 0.0140 0.0082 0.0383 0.0123 0.0238 0.000 0.0219 0.0378 0.0339 0.0125 0.0208 0.0374 0.0429 0.0281 0.0337 0.0185 0.0243 0.0161 0.0383 0.0197 0.0178 0.0378 0.0098 0.0168 0.0429 0.0435 0.0329 0.0367 0.0250 0.0400 0.0382 0.0339 0.0333 0.0468 0.0232 0.0408 0.0376 0.0391 0.0380 0.0193 0.0441 0.0376 0.0437 0.0470 0.0041 0.0443 0.0444 0.0406 0.0279 0.0409 0.0207 0.0449 0.0478 0.0361 0.0406 0.0359 0.0231 0.0319 0.041 0.0062 0.0125 0.0161 0.0384 0.000 0.0038 0.0020 0.002 0.0000 0.0019 0.0061 0.0060 0.004 0.0000 0.0080 0.0082 0.0020 0.0041 0.0061 0.0061 0.0040 0.0059 0.0348 0.0249 0.0277 0.0138 0.0142 0.0292 0.040 0.0193 0.0488 0.0307 0.0277 0.0357 0.0309 0.0408 0.0480 0.0460 0.0248 0.0472 0.0198 0.0202 0.0233 0.0435 0.0442 0.0239 0.0449 0.0253 0.0335 0.0431 0.0337 0.0422 0.0081 0.0498 0.0313 0.0364 0.0385 0.0452 0.0475 0.0167 0.0485 0.0354

Close cluster

# stopCluster(cl)

PCA plot of pathways deemed significant in MPEA but not GSEA

library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()) 

# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP"

## [1] "AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN"

## [1] "AMIT_EGF_RESPONSE_40_MCF10A"

## [1] "BASAKI_YBX1_TARGETS_UP"

## [1] "BERNARD_PPAPDC1B_TARGETS_UP"

## [1] "BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN"

## [1] "BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP"

## [1] "BHAT_ESR1_TARGETS_VIA_AKT1_UP"

## [1] "BILD_MYC_ONCOGENIC_SIGNATURE"

## [1] "BIOCARTA_CARDIACEGF_PATHWAY"

## [1] "BIOCARTA_CDC42RAC_PATHWAY"

## [1] "BIOCARTA_EDG1_PATHWAY"

## [1] "BIOCARTA_P53HYPOXIA_PATHWAY"

## [1] "BIOCARTA_PAR1_PATHWAY"

## [1] "BIOCARTA_PTDINS_PATHWAY"

## [1] "BIOCARTA_RACCYCD_PATHWAY"

## [1] "BIOCARTA_RAS_PATHWAY"

## [1] "BOCHKIS_FOXA2_TARGETS"

## [1] "BORCZUK_MALIGNANT_MESOTHELIOMA_UP"

## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN"

## [1] "BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP"

## [1] "BROWNE_HCMV_INFECTION_48HR_UP"

## [1] "BROWNE_HCMV_INFECTION_4HR_DN"

## [1] "BROWNE_HCMV_INFECTION_6HR_DN"

## [1] "BRUECKNER_TARGETS_OF_MIRLET7A3_UP"

## [1] "BURTON_ADIPOGENESIS_6"

## [1] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN"

## [1] "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS"

## [1] "CADWELL_ATG16L1_TARGETS_DN"

## [1] "CAFFAREL_RESPONSE_TO_THC_DN"

## [1] "CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP"

## [1] "CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP"

## [1] "CHEBOTAEV_GR_TARGETS_DN"

## [1] "CHEN_ETV5_TARGETS_TESTIS"

## [1] "COATES_MACROPHAGE_M1_VS_M2_DN"

## [1] "COATES_MACROPHAGE_M1_VS_M2_UP"

## [1] "CUI_GLUCOSE_DEPRIVATION"

## [1] "DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP"

## [1] "DAZARD_RESPONSE_TO_UV_NHEK_DN"

## [1] "DE_YY1_TARGETS_UP"

## [1] "DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN"

## [1] "DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER"

## [1] "ENGELMANN_CANCER_PROGENITORS_DN"

## [1] "ENGELMANN_CANCER_PROGENITORS_UP"

## [1] "ENK_UV_RESPONSE_KERATINOCYTE_DN"

## [1] "FARMER_BREAST_CANCER_APOCRINE_VS_BASAL"

## [1] "FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL"

## [1] "FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS"

## [1] "FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN"

## [1] "FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP"

## [1] "FORTSCHEGGER_PHF8_TARGETS_UP"

## [1] "FOSTER_TOLERANT_MACROPHAGE_UP"

## [1] "FRIDMAN_IMMORTALIZATION_DN"

## [1] "FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP"

## [1] "GAJATE_RESPONSE_TO_TRABECTEDIN_UP"

## [1] "GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN"

## [1] "GARY_CD5_TARGETS_DN"

## [1] "GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP"

## [1] "GEISS_RESPONSE_TO_DSRNA_DN"

## [1] "GENTILE_UV_LOW_DOSE_UP"

## [1] "GEORGES_TARGETS_OF_MIR192_AND_MIR215"

## [1] "GOLUB_ALL_VS_AML_DN"

## [1] "GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP"

## [1] "GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN"

## [1] "GUILLAUMOND_KLF10_TARGETS_DN"

## [1] "GUTIERREZ_MULTIPLE_MYELOMA_UP"

## [1] "HASLINGER_B_CLL_WITH_MUTATED_VH_GENES"

## [1] "HEIDENBLAD_AMPLICON_12P11_12_UP"

## [1] "HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS"

## [1] "HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN"

## [1] "HORTON_SREBF_TARGETS"

## [1] "HOUSTIS_ROS"

## [1] "HU_ANGIOGENESIS_DN"

## [1] "ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN"

## [1] "IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP"

## [1] "JAEGER_METASTASIS_DN"

## [1] "JOHNSTONE_PARVB_TARGETS_3_UP"

## [1] "JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP"

## [1] "KASLER_HDAC7_TARGETS_1_DN"

## [1] "KEEN_RESPONSE_TO_ROSIGLITAZONE_UP"

## [1] "KEGG_COLORECTAL_CANCER"

## [1] "KEGG_PYRIMIDINE_METABOLISM"

## [1] "KEGG_RNA_POLYMERASE"

## [1] "KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"

## [1] "KEGG_STEROID_BIOSYNTHESIS"

## [1] "KENNY_CTNNB1_TARGETS_DN"

## [1] "KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP"

## [1] "LABBE_WNT3A_TARGETS_DN"

## [1] "LAMB_CCND1_TARGETS"

## [1] "LEE_DIFFERENTIATING_T_LYMPHOCYTE"

## [1] "LEE_TARGETS_OF_PTCH1_AND_SUFU_DN"

## [1] "LEIN_CHOROID_PLEXUS_MARKERS"

## [1] "LENAOUR_DENDRITIC_CELL_MATURATION_DN"

## [1] "LI_INDUCED_T_TO_NATURAL_KILLER_DN"

## [1] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP"

## [1] "LIN_NPAS4_TARGETS_UP"

## [1] "LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q"

## [1] "LIU_PROSTATE_CANCER_UP"

## [1] "LIU_SOX4_TARGETS_UP"

## [1] "MA_MYELOID_DIFFERENTIATION_DN"

## [1] "MACLACHLAN_BRCA1_TARGETS_UP"

## [1] "MANALO_HYPOXIA_DN"

## [1] "MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5"

## [1] "MARKS_HDAC_TARGETS_UP"

## [1] "MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP"

## [1] "MASSARWEH_RESPONSE_TO_ESTRADIOL"

## [1] "MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN"

## [1] "MCCLUNG_COCAINE_REWARD_5D"

## [1] "MENSE_HYPOXIA_UP"

## [1] "MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED"

## [1] "MIKKELSEN_ES_ICP_WITH_H3K4ME3"

## [1] "MISSIAGLIA_REGULATED_BY_METHYLATION_UP"

## [1] "MITSIADES_RESPONSE_TO_APLIDIN_UP"

## [1] "MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN"

## [1] "MOREIRA_RESPONSE_TO_TSA_UP"

## [1] "MORI_SMALL_PRE_BII_LYMPHOCYTE_UP"

## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP"

## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP"

## [1] "MULLIGHAN_NPM1_SIGNATURE_3_UP"

## [1] "MURAKAMI_UV_RESPONSE_24HR"

## [1] "MURAKAMI_UV_RESPONSE_6HR_DN"

## [1] "NADLER_HYPERGLYCEMIA_AT_OBESITY"

## [1] "NAGASHIMA_NRG1_SIGNALING_DN"

## [1] "NOJIMA_SFRP2_TARGETS_UP"

## [1] "NUYTTEN_NIPP1_TARGETS_UP"

## [1] "ODONNELL_METASTASIS_DN"

## [1] "ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP"

## [1] "OISHI_CHOLANGIOMA_STEM_CELL_LIKE_DN"

## [1] "ONDER_CDH1_TARGETS_1_UP"

## [1] "OUILLETTE_CLL_13Q14_DELETION_DN"

## [1] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7"

## [1] "PENG_RAPAMYCIN_RESPONSE_UP"

## [1] "PETRETTO_CARDIAC_HYPERTROPHY"

## [1] "PETRETTO_HEART_MASS_QTL_CIS_DN"

## [1] "PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP"

## [1] "PETROVA_PROX1_TARGETS_UP"

## [1] "PID_AVB3_INTEGRIN_PATHWAY"

## [1] "PID_AVB3_OPN_PATHWAY"

## [1] "PID_ECADHERIN_KERATINOCYTE_PATHWAY"

## [1] "PID_ECADHERIN_NASCENT_AJ_PATHWAY"

## [1] "PID_EPHA_FWDPATHWAY"

## [1] "PID_EPHA2_FWD_PATHWAY"

## [1] "PID_IL4_2PATHWAY"

## [1] "PID_LIS1_PATHWAY"

## [1] "PID_P53_REGULATION_PATHWAY"

## [1] "PID_PRL_SIGNALING_EVENTS_PATHWAY"

## [1] "PID_PTP1B_PATHWAY"

## [1] "PID_S1P_S1P1_PATHWAY"

## [1] "PID_S1P_S1P2_PATHWAY"

## [1] "PID_S1P_S1P3_PATHWAY"

## [1] "PID_SYNDECAN_4_PATHWAY"

## [1] "PID_TGFBR_PATHWAY"

## [1] "PID_VEGFR1_2_PATHWAY"

## [1] "PID_WNT_NONCANONICAL_PATHWAY"

## [1] "PLASARI_NFIC_TARGETS_BASAL_UP"

## [1] "PLASARI_TGFB1_TARGETS_10HR_DN"

## [1] "PUJANA_BRCA2_PCC_NETWORK"

## [1] "QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2"

## [1] "RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP"

## [1] "RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN"

## [1] "REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT"

## [1] "REACTOME_CHOLESTEROL_BIOSYNTHESIS"

## [1] "REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX"

## [1] "REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX"

## [1] "REACTOME_G_ALPHA1213_SIGNALLING_EVENTS"

## [1] "REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA"

## [1] "REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING"

## [1] "REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE"

## [1] "REACTOME_MICRORNA_MIRNA_BIOGENESIS"

## [1] "REACTOME_MRNA_SPLICING_MINOR_PATHWAY"

## [1] "REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING"

## [1] "REACTOME_PEROXISOMAL_LIPID_METABOLISM"

## [1] "REACTOME_PI3K_AKT_ACTIVATION"

## [1] "REACTOME_REGULATORY_RNA_PATHWAYS"

## [1] "REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING"

## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION"

## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER"

## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER"

## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION"

## [1] "REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING"

## [1] "REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE"

## [1] "REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT"

## [1] "RICKMAN_METASTASIS_UP"

## [1] "RIGGI_EWING_SARCOMA_PROGENITOR_DN"

## [1] "RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP"

## [1] "RODWELL_AGING_KIDNEY_NO_BLOOD_DN"

## [1] "ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP"

## [1] "SA_TRKA_RECEPTOR"

## [1] "SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN"

## [1] "SANSOM_APC_TARGETS_DN"

## [1] "SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1"

## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP"

## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP"

## [1] "SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP"

## [1] "SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY"

## [1] "SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP"

## [1] "SHEN_SMARCA2_TARGETS_UP"

## [1] "SHEPARD_CRUSH_AND_BURN_MUTANT_UP"

## [1] "SHI_SPARC_TARGETS_UP"

## [1] "SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN"

## [1] "SMITH_TERT_TARGETS_DN"

## [1] "TARTE_PLASMA_CELL_VS_PLASMABLAST_DN"

## [1] "TIAN_TNF_SIGNALING_NOT_VIA_NFKB"

## [1] "TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP"

## [1] "UEDA_PERIFERAL_CLOCK"

## [1] "VANTVEER_BREAST_CANCER_ESR1_UP"

## [1] "VARELA_ZMPSTE24_TARGETS_UP"

## [1] "VERHAAK_GLIOBLASTOMA_NEURAL"

## [1] "VERRECCHIA_EARLY_RESPONSE_TO_TGFB1"

## [1] "WALLACE_PROSTATE_CANCER_RACE_UP"

## [1] "WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN"

## [1] "WANG_SMARCE1_TARGETS_UP"

## [1] "WANG_TARGETS_OF_MLL_CBP_FUSION_DN"

## [1] "WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP"

## [1] "WHITFIELD_CELL_CYCLE_G2"

## [1] "WIERENGA_STAT5A_TARGETS_GROUP1"

## [1] "WIERENGA_STAT5A_TARGETS_GROUP2"

## [1] "WIERENGA_STAT5A_TARGETS_UP"

## [1] "WINNEPENNINCKX_MELANOMA_METASTASIS_DN"

## [1] "WINZEN_DEGRADED_VIA_KHSRP"

## [1] "YAGI_AML_RELAPSE_PROGNOSIS"

## [1] "YAGI_AML_WITH_T_8_21_TRANSLOCATION"

## [1] "YAMASHITA_METHYLATED_IN_PROSTATE_CANCER"

## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1"

## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5"

## [1] "ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN"

## [1] "ZHANG_TLX_TARGETS_60HR_DN"

## [1] "ZHENG_FOXP3_TARGETS_IN_THYMUS_UP"

PCA plot of pathways deemed significant in GSEA but not MPEA

rownames(gsea_results_significant)
##   [1] "LUI_TARGETS_OF_PAX8_PPARG_FUSION"                                                                                          
##   [2] "MOOTHA_VOXPHOS"                                                                                                            
##   [3] "LUI_THYROID_CANCER_CLUSTER_3"                                                                                              
##   [4] "ANDERSEN_LIVER_CANCER_KRT19_UP"                                                                                            
##   [5] "REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_"
##   [6] "POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN"                                                                                      
##   [7] "MCBRYAN_PUBERTAL_BREAST_3_4WK_DN"                                                                                          
##   [8] "REACTOME_INFLUENZA_LIFE_CYCLE"                                                                                             
##   [9] "LANDIS_ERBB2_BREAST_TUMORS_324_UP"                                                                                         
##  [10] "KEGG_ALZHEIMERS_DISEASE"                                                                                                   
##  [11] "REACTOME_METABOLISM_OF_RNA"                                                                                                
##  [12] "CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP"                                                                                       
##  [13] "REACTOME_RESPIRATORY_ELECTRON_TRANSPORT"                                                                                   
##  [14] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP"                                                                                     
##  [15] "FERRANDO_TAL1_NEIGHBORS"                                                                                                   
##  [16] "REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY"                                                         
##  [17] "REACTOME_METABOLISM_OF_MRNA"                                                                                               
##  [18] "PECE_MAMMARY_STEM_CELL_UP"                                                                                                 
##  [19] "KEGG_NUCLEOTIDE_EXCISION_REPAIR"                                                                                           
##  [20] "LANDIS_ERBB2_BREAST_TUMORS_65_UP"                                                                                          
##  [21] "KEGG_OXIDATIVE_PHOSPHORYLATION"                                                                                            
##  [22] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13"                                                                          
##  [23] "TONG_INTERACT_WITH_PTTG1"                                                                                                  
##  [24] "EHLERS_ANEUPLOIDY_UP"                                                                                                      
##  [25] "YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP"                                                                                      
##  [26] "KANNAN_TP53_TARGETS_DN"                                                                                                    
##  [27] "DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN"                                                                                      
##  [28] "MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN"                                                                                      
##  [29] "REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX"                                                    
##  [30] "REACTOME_TRANSLATION"                                                                                                      
##  [31] "REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES"                                                 
##  [32] "TAKAO_RESPONSE_TO_UVB_RADIATION_UP"                                                                                        
##  [33] "BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN"                                                                                  
##  [34] "KEGG_HUNTINGTONS_DISEASE"                                                                                                  
##  [35] "REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE"                                                      
##  [36] "HUMMERICH_BENIGN_SKIN_TUMOR_UP"                                                                                            
##  [37] "HSIAO_HOUSEKEEPING_GENES"                                                                                                  
##  [38] "JAZAG_TGFB1_SIGNALING_UP"                                                                                                  
##  [39] "BAE_BRCA1_TARGETS_UP"                                                                                                      
##  [40] "KEGG_RIBOSOME"                                                                                                             
##  [41] "NUTT_GBM_VS_AO_GLIOMA_DN"                                                                                                  
##  [42] "MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP"                                                                                       
##  [43] "KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN"                                                                                     
##  [44] "REACTOME_METABOLISM_OF_PROTEINS"                                                                                           
##  [45] "BILANGES_SERUM_RESPONSE_TRANSLATION"                                                                                       
##  [46] "REACTOME_NUCLEOTIDE_EXCISION_REPAIR"                                                                                       
##  [47] "LANDIS_BREAST_CANCER_PROGRESSION_UP"                                                                                       
##  [48] "WONG_MITOCHONDRIA_GENE_MODULE"                                                                                             
##  [49] "NAKAYAMA_FGF2_TARGETS"                                                                                                     
##  [50] "HUNSBERGER_EXERCISE_REGULATED_GENES"                                                                                       
##  [51] "REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER"                                                                                 
##  [52] "LUI_THYROID_CANCER_PAX8_PPARG_DN"                                                                                          
##  [53] "WENG_POR_TARGETS_GLOBAL_UP"                                                                                                
##  [54] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN"                                                                                     
##  [55] "MORI_IMMATURE_B_LYMPHOCYTE_UP"                                                                                             
##  [56] "REACTOME_PEPTIDE_CHAIN_ELONGATION"                                                                                         
##  [57] "NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON"                                                                                  
##  [58] "IRITANI_MAD1_TARGETS_DN"                                                                                                   
##  [59] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17"                                                                          
##  [60] "LEE_LIVER_CANCER_SURVIVAL_DN"                                                                                              
##  [61] "REACTOME_SIGNAL_AMPLIFICATION"                                                                                             
##  [62] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP"                                                                     
##  [63] "WANG_RESPONSE_TO_FORSKOLIN_UP"                                                                                             
##  [64] "JIANG_AGING_HYPOTHALAMUS_UP"                                                                                               
##  [65] "PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN"                                                                                    
##  [66] "HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP"                                                                                   
##  [67] "KEGG_BASAL_TRANSCRIPTION_FACTORS"                                                                                          
##  [68] "OSMAN_BLADDER_CANCER_DN"                                                                                                   
##  [69] "YANG_BREAST_CANCER_ESR1_UP"                                                                                                
##  [70] "ZHAN_MULTIPLE_MYELOMA_HP_UP"                                                                                               
##  [71] "PARK_HSC_MARKERS"                                                                                                          
##  [72] "REACTOME_MRNA_CAPPING"                                                                                                     
##  [73] "GROSS_HYPOXIA_VIA_HIF1A_UP"                                                                                                
##  [74] "REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS"                                                                      
##  [75] "WANG_TUMOR_INVASIVENESS_UP"                                                                                                
##  [76] "REACTOME_GLOBAL_GENOMIC_NER_GG_NER"                                                                                        
##  [77] "GEORGES_CELL_CYCLE_MIR192_TARGETS"                                                                                         
##  [78] "MAINA_VHL_TARGETS_DN"                                                                                                      
##  [79] "CHEN_PDGF_TARGETS"                                                                                                         
##  [80] "SCHRAMM_INHBA_TARGETS_DN"                                                                                                  
##  [81] "FAELT_B_CLL_WITH_VH3_21_DN"                                                                                                
##  [82] "BOUDOUKHA_BOUND_BY_IGF2BP2"                                                                                                
##  [83] "NATSUME_RESPONSE_TO_INTERFERON_BETA_DN"                                                                                    
##  [84] "REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE"                                                                                     
##  [85] "GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN"                                                                                        
##  [86] "MURAKAMI_UV_RESPONSE_1HR_UP"                                                                                               
##  [87] "PID_PI3K_PLC_TRK_PATHWAY"                                                                                                  
##  [88] "REACTOME_ADP_SIGNALLING_THROUGH_P2RY1"                                                                                     
##  [89] "WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP"                                                                         
##  [90] "CHANGOLKAR_H2AFY_TARGETS_UP"                                                                                               
##  [91] "BIDUS_METASTASIS_DN"                                                                                                       
##  [92] "BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP"                                                                               
##  [93] "PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN"                                                                              
##  [94] "BORLAK_LIVER_CANCER_EGF_UP"                                                                                                
##  [95] "REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS"                                                                                      
##  [96] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9"                                                                           
##  [97] "KIM_MYC_AMPLIFICATION_TARGETS_UP"                                                                                          
##  [98] "LINDGREN_BLADDER_CANCER_CLUSTER_1_UP"                                                                                      
##  [99] "CHANGOLKAR_H2AFY_TARGETS_DN"                                                                                               
## [100] "HORIUCHI_WTAP_TARGETS_DN"                                                                                                  
## [101] "SASAKI_ADULT_T_CELL_LEUKEMIA"                                                                                              
## [102] "GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN"                                                                                
## [103] "REACTOME_DNA_REPAIR"                                                                                                       
## [104] "REACTOME_INTEGRATION_OF_ENERGY_METABOLISM"                                                                                 
## [105] "PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP"                                                                                      
## [106] "DELASERNA_MYOD_TARGETS_UP"                                                                                                 
## [107] "KASLER_HDAC7_TARGETS_2_DN"                                                                                                 
## [108] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN"                                                                                 
## [109] "SHIN_B_CELL_LYMPHOMA_CLUSTER_8"                                                                                            
## [110] "DOANE_BREAST_CANCER_ESR1_DN"                                                                                               
## [111] "BIOCARTA_AGR_PATHWAY"                                                                                                      
## [112] "REACTOME_RNA_POL_I_PROMOTER_OPENING"                                                                                       
## [113] "REACTOME_HDL_MEDIATED_LIPID_TRANSPORT"                                                                                     
## [114] "REACTOME_MEIOTIC_SYNAPSIS"                                                                                                 
## [115] "FAELT_B_CLL_WITH_VH3_21_UP"                                                                                                
## [116] "KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3"                                                                                   
## [117] "HASLINGER_B_CLL_WITH_6Q21_DELETION"                                                                                        
## [118] "KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN"                                                                      
## [119] "KEGG_PPAR_SIGNALING_PATHWAY"                                                                                               
## [120] "REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE"                                                 
## [121] "MIKKELSEN_MEF_LCP_WITH_H3K27ME3"                                                                                           
## [122] "XU_GH1_EXOGENOUS_TARGETS_DN"                                                                                               
## [123] "ABE_VEGFA_TARGETS_2HR"                                                                                                     
## [124] "FIGUEROA_AML_METHYLATION_CLUSTER_1_DN"                                                                                     
## [125] "REACTOME_LIPOPROTEIN_METABOLISM"                                                                                           
## [126] "BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN"                                                                                    
## [127] "BIOCARTA_UCALPAIN_PATHWAY"                                                                                                 
## [128] "ST_T_CELL_SIGNAL_TRANSDUCTION"                                                                                             
## [129] "DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY"                                                                                    
## [130] "OHGUCHI_LIVER_HNF4A_TARGETS_UP"                                                                                            
## [131] "HUMMERICH_MALIGNANT_SKIN_TUMOR_DN"                                                                                         
## [132] "CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP"                                                                                       
## [133] "PID_NCADHERIN_PATHWAY"                                                                                                     
## [134] "HUMMERICH_BENIGN_SKIN_TUMOR_DN"                                                                                            
## [135] "REACTOME_PACKAGING_OF_TELOMERE_ENDS"                                                                                       
## [136] "LEI_HOXC8_TARGETS_DN"                                                                                                      
## [137] "REACTOME_MEIOSIS"                                                                                                          
## [138] "PID_BARD1_PATHWAY"                                                                                                         
## [139] "FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP"                                                                                 
## [140] "BIOCARTA_MAL_PATHWAY"                                                                                                      
## [141] "XU_AKT1_TARGETS_6HR"                                                                                                       
## [142] "PID_INSULIN_GLUCOSE_PATHWAY"                                                                                               
## [143] "REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS"                                                                           
## [144] "SA_B_CELL_RECEPTOR_COMPLEXES"                                                                                              
## [145] "SCHEIDEREIT_IKK_INTERACTING_PROTEINS"                                                                                      
## [146] "SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER"                                                                         
## [147] "REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM"                                                                               
## [148] "ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN"                                                                                      
## [149] "GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP"                                                                                     
## [150] "BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP"                                                                                  
## [151] "RIZ_ERYTHROID_DIFFERENTIATION_HEMGN"                                                                                       
## [152] "MEISSNER_BRAIN_HCP_WITH_H3K27ME3"                                                                                          
## [153] "REACTOME_SEMAPHORIN_INTERACTIONS"                                                                                          
## [154] "KUMAR_AUTOPHAGY_NETWORK"                                                                                                   
## [155] "SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN"                                                                                   
## [156] "KENNY_CTNNB1_TARGETS_UP"                                                                                                   
## [157] "OXFORD_RALA_OR_RALB_TARGETS_UP"                                                                                            
## [158] "LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP"                                                                                       
## [159] "MIKKELSEN_NPC_HCP_WITH_H3K27ME3"                                                                                           
## [160] "BIOCARTA_HER2_PATHWAY"                                                                                                     
## [161] "FIGUEROA_AML_METHYLATION_CLUSTER_3_DN"                                                                                     
## [162] "KYNG_DNA_DAMAGE_BY_4NQO"                                                                                                   
## [163] "MULLIGHAN_NPM1_SIGNATURE_3_DN"                                                                                             
## [164] "PID_IL23_PATHWAY"                                                                                                          
## [165] "REACTOME_MEIOTIC_RECOMBINATION"                                                                                            
## [166] "MIKKELSEN_MCV6_HCP_WITH_H3K27ME3"                                                                                          
## [167] "REACTOME_CHROMOSOME_MAINTENANCE"                                                                                           
## [168] "CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP"                                                                                    
## [169] "QI_HYPOXIA"                                                                                                                
## [170] "SMID_BREAST_CANCER_ERBB2_UP"
for (name in (Significant_in_GSEA_not_in_dcor)){
  strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
  expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
  genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
  genotypes_category <- as.data.frame(genotypes_category)
  print(name)
  print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name")) 
  
  # pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
  # biplot.pcoa(pcoa.obj)
}
## [1] "LUI_TARGETS_OF_PAX8_PPARG_FUSION"

## [1] "LUI_THYROID_CANCER_CLUSTER_3"

## [1] "ANDERSEN_LIVER_CANCER_KRT19_UP"

## [1] "REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_"

## [1] "POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN"

## [1] "MCBRYAN_PUBERTAL_BREAST_3_4WK_DN"

## [1] "REACTOME_INFLUENZA_LIFE_CYCLE"

## [1] "LANDIS_ERBB2_BREAST_TUMORS_324_UP"

## [1] "KEGG_ALZHEIMERS_DISEASE"

## [1] "REACTOME_METABOLISM_OF_RNA"

## [1] "CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP"

## [1] "REACTOME_RESPIRATORY_ELECTRON_TRANSPORT"

## [1] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP"

## [1] "REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY"

## [1] "REACTOME_METABOLISM_OF_MRNA"

## [1] "PECE_MAMMARY_STEM_CELL_UP"

## [1] "KEGG_NUCLEOTIDE_EXCISION_REPAIR"

## [1] "TONG_INTERACT_WITH_PTTG1"

## [1] "EHLERS_ANEUPLOIDY_UP"

## [1] "YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP"

## [1] "KANNAN_TP53_TARGETS_DN"

## [1] "DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN"

## [1] "MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN"

## [1] "REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX"

## [1] "REACTOME_TRANSLATION"

## [1] "REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES"

## [1] "TAKAO_RESPONSE_TO_UVB_RADIATION_UP"

## [1] "BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN"

## [1] "REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE"

## [1] "HUMMERICH_BENIGN_SKIN_TUMOR_UP"

## [1] "HSIAO_HOUSEKEEPING_GENES"

## [1] "JAZAG_TGFB1_SIGNALING_UP"

## [1] "BAE_BRCA1_TARGETS_UP"

## [1] "KEGG_RIBOSOME"

## [1] "NUTT_GBM_VS_AO_GLIOMA_DN"

## [1] "MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP"

## [1] "KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN"

## [1] "REACTOME_METABOLISM_OF_PROTEINS"

## [1] "BILANGES_SERUM_RESPONSE_TRANSLATION"

## [1] "LANDIS_BREAST_CANCER_PROGRESSION_UP"

## [1] "NAKAYAMA_FGF2_TARGETS"

## [1] "HUNSBERGER_EXERCISE_REGULATED_GENES"

## [1] "LUI_THYROID_CANCER_PAX8_PPARG_DN"

## [1] "WENG_POR_TARGETS_GLOBAL_UP"

## [1] "REACTOME_PEPTIDE_CHAIN_ELONGATION"

## [1] "NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON"

## [1] "IRITANI_MAD1_TARGETS_DN"

## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17"

## [1] "LEE_LIVER_CANCER_SURVIVAL_DN"

## [1] "REACTOME_SIGNAL_AMPLIFICATION"

## [1] "WANG_RESPONSE_TO_FORSKOLIN_UP"

## [1] "JIANG_AGING_HYPOTHALAMUS_UP"

## [1] "PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN"

## [1] "HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP"

## [1] "KEGG_BASAL_TRANSCRIPTION_FACTORS"

## [1] "OSMAN_BLADDER_CANCER_DN"

## [1] "YANG_BREAST_CANCER_ESR1_UP"

## [1] "ZHAN_MULTIPLE_MYELOMA_HP_UP"

## [1] "PARK_HSC_MARKERS"

## [1] "REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS"

## [1] "WANG_TUMOR_INVASIVENESS_UP"

## [1] "REACTOME_GLOBAL_GENOMIC_NER_GG_NER"

## [1] "GEORGES_CELL_CYCLE_MIR192_TARGETS"

## [1] "MAINA_VHL_TARGETS_DN"

## [1] "CHEN_PDGF_TARGETS"

## [1] "SCHRAMM_INHBA_TARGETS_DN"

## [1] "FAELT_B_CLL_WITH_VH3_21_DN"

## [1] "BOUDOUKHA_BOUND_BY_IGF2BP2"

## [1] "NATSUME_RESPONSE_TO_INTERFERON_BETA_DN"

## [1] "REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE"

## [1] "GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN"

## [1] "MURAKAMI_UV_RESPONSE_1HR_UP"

## [1] "PID_PI3K_PLC_TRK_PATHWAY"

## [1] "REACTOME_ADP_SIGNALLING_THROUGH_P2RY1"

## [1] "WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP"

## [1] "CHANGOLKAR_H2AFY_TARGETS_UP"

## [1] "BIDUS_METASTASIS_DN"

## [1] "BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP"

## [1] "PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN"

## [1] "BORLAK_LIVER_CANCER_EGF_UP"

## [1] "REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS"

## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9"

## [1] "KIM_MYC_AMPLIFICATION_TARGETS_UP"

## [1] "LINDGREN_BLADDER_CANCER_CLUSTER_1_UP"

## [1] "CHANGOLKAR_H2AFY_TARGETS_DN"

## [1] "HORIUCHI_WTAP_TARGETS_DN"

## [1] "SASAKI_ADULT_T_CELL_LEUKEMIA"

## [1] "GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN"

## [1] "REACTOME_INTEGRATION_OF_ENERGY_METABOLISM"

## [1] "DELASERNA_MYOD_TARGETS_UP"

## [1] "KASLER_HDAC7_TARGETS_2_DN"

## [1] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN"

## [1] "SHIN_B_CELL_LYMPHOMA_CLUSTER_8"

## [1] "DOANE_BREAST_CANCER_ESR1_DN"

## [1] "BIOCARTA_AGR_PATHWAY"

## [1] "REACTOME_RNA_POL_I_PROMOTER_OPENING"

## [1] "REACTOME_HDL_MEDIATED_LIPID_TRANSPORT"

## [1] "FAELT_B_CLL_WITH_VH3_21_UP"

## [1] "KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3"

## [1] "HASLINGER_B_CLL_WITH_6Q21_DELETION"

## [1] "KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN"

## [1] "KEGG_PPAR_SIGNALING_PATHWAY"

## [1] "REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE"

## [1] "MIKKELSEN_MEF_LCP_WITH_H3K27ME3"

## [1] "XU_GH1_EXOGENOUS_TARGETS_DN"

## [1] "ABE_VEGFA_TARGETS_2HR"

## [1] "FIGUEROA_AML_METHYLATION_CLUSTER_1_DN"

## [1] "REACTOME_LIPOPROTEIN_METABOLISM"

## [1] "BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN"

## [1] "BIOCARTA_UCALPAIN_PATHWAY"

## [1] "ST_T_CELL_SIGNAL_TRANSDUCTION"

## [1] "DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY"

## [1] "HUMMERICH_MALIGNANT_SKIN_TUMOR_DN"

## [1] "CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP"

## [1] "PID_NCADHERIN_PATHWAY"

## [1] "HUMMERICH_BENIGN_SKIN_TUMOR_DN"

## [1] "REACTOME_PACKAGING_OF_TELOMERE_ENDS"

## [1] "LEI_HOXC8_TARGETS_DN"

## [1] "PID_BARD1_PATHWAY"

## [1] "FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP"

## [1] "BIOCARTA_MAL_PATHWAY"

## [1] "XU_AKT1_TARGETS_6HR"

## [1] "PID_INSULIN_GLUCOSE_PATHWAY"

## [1] "REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS"

## [1] "SA_B_CELL_RECEPTOR_COMPLEXES"

## [1] "SCHEIDEREIT_IKK_INTERACTING_PROTEINS"

## [1] "REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM"

## [1] "ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN"

## [1] "BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP"

## [1] "RIZ_ERYTHROID_DIFFERENTIATION_HEMGN"

## [1] "MEISSNER_BRAIN_HCP_WITH_H3K27ME3"

## [1] "REACTOME_SEMAPHORIN_INTERACTIONS"

## [1] "KUMAR_AUTOPHAGY_NETWORK"

## [1] "SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN"

## [1] "KENNY_CTNNB1_TARGETS_UP"

## [1] "OXFORD_RALA_OR_RALB_TARGETS_UP"

## [1] "LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP"

## [1] "MIKKELSEN_NPC_HCP_WITH_H3K27ME3"

## [1] "BIOCARTA_HER2_PATHWAY"

## [1] "FIGUEROA_AML_METHYLATION_CLUSTER_3_DN"

## [1] "KYNG_DNA_DAMAGE_BY_4NQO"

## [1] "MULLIGHAN_NPM1_SIGNATURE_3_DN"

## [1] "PID_IL23_PATHWAY"

## [1] "REACTOME_MEIOTIC_RECOMBINATION"

## [1] "MIKKELSEN_MCV6_HCP_WITH_H3K27ME3"

## [1] "CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP"

## [1] "QI_HYPOXIA"